I designed my preamp to be able to do either one, because I had a lot of these questions as well. It has a pre-blend slot for each pickup and a post blend slot. You can plug any filter/eq module into any slot. I've tried putting the 3 band parametric EQ on each pickup, and what gets overwhelmed is me! It's almost impossible to do anything predictable! The classic LPF filters are the best for per-pickup. They are simple and repeatable enough to be useful.
You are dead on regarding phase. Because the signals of the pickups are substantially similar, and because the phase gets inverted near the peak, there is an almost complete cancellation at certain filter settings and frequencies. If the filters are at the exact same frequency, then the peak stays up full, but when they are slightly apart, both peaks end up being at about half the level. As you move farther apart in frequency, the peaks come back up, but there is a region in between where there is phase cancellation, which gives a kind of scooped sound. It's all very useful and interesting sounding, but I think some folks think of the two filter responses simply being added together, which isn't the case. With a post blend filter/eq, you can't hear the phase shift, so it sounds exactly like what you picture in your head. Of course the blend dramatically changes this, because you are turning down one of the signals that is cancelling the other. That's why you can keep a lot more treble if you roll the blend very slightly toward the filter that is set up high.
As for the sensing location, everything is still Jazz Bass. You get the same mellowing of harmonics in the middle, etc with either setup.
Noise is no different with per-pickup. In fact it seems like it is quieter with two filters. Maybe a real EE can comment, but I think the noise partially cancels (in the same way that two 100k resistors in parallel are as quiet as a 50k resistor). Page 37 of Self (third edition) discusses it with Multi-Path Amplifiers, which are incredibly quiet. I use the same circuit for blend, so that would explain why it seems quieter than a single EQ. Curiously, if you are using single-coils, you can balance noise with the filters! You can set the blend off center, then by adjusting the filters you are essentially trimming the gain and you can dial the noise back out! I use it a lot.
Presets for sure. That's why I have a bypass switch socket on every filter slot. It's super nice to be able to toggle one or both filters on or off on the fly (you could do a full eq per pickup and replace the blend pot with a switch to make things less confusing). I'm a big fan of bypass switches.
